WriteNC.hpp

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/**
 * MOAB, a Mesh-Oriented datABase, is a software component for creating,
 * storing and accessing finite element mesh data.
 *
 * Copyright 2004 Sandia Corporation.  Under the terms of Contract
 * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
 * retains certain rights in this software.
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 *
 */
 
#ifndef WRITENC_HPP_
#define WRITENC_HPP_
 
#ifndef IS_BUILDING_MB
#error "WriteNC.hpp isn't supposed to be included into an application"
#endif
 
#include <vector>
#include <map>
#include <set>
#include <string>
 
#include "moab/WriterIface.hpp"
#include "moab/ScdInterface.hpp"
#include "DebugOutput.hpp"
 
#ifdef MOAB_HAVE_MPI
#include "moab_mpi.h"
#include "moab/ParallelComm.hpp"
#endif
 
#ifdef MOAB_HAVE_PNETCDF
#include "pnetcdf.h"
#define NCFUNC( func ) ncmpi_##func
 
//! Collective I/O mode put
#define NCFUNCAP( func ) ncmpi_put##func##_all
 
//! Independent I/O mode put
#define NCFUNCP( func ) ncmpi_put##func
 
//! Nonblocking put (request aggregation)
#define NCFUNCREQP( func ) ncmpi_iput##func
 
#define NCDF_SIZE MPI_Offset
#define NCDF_DIFF MPI_Offset
#else
#include "netcdf.h"
#define NCFUNC( func )   nc_##func
#define NCFUNCAP( func ) nc_put##func
#define NCFUNCP( func )  nc_put##func
#define NCDF_SIZE        size_t
#define NCDF_DIFF        ptrdiff_t
#endif
 
namespace moab
{
 
class WriteUtilIface;
class NCWriteHelper;
 
/**
 * \brief Export NC files.
 */
class WriteNC : public WriterIface
{
    friend class NCWriteHelper;
    friend class ScdNCWriteHelper;
    friend class UcdNCWriteHelper;
    friend class NCWriteEuler;
    friend class NCWriteFV;
    friend class NCWriteHOMME;
    friend class NCWriteMPAS;
    friend class NCWriteGCRM;
 
  public:
    //! Factory method
    static WriterIface* factory( Interface* );
 
    //! Constructor
    WriteNC( Interface* impl = NULL );
 
    //! Destructor
    virtual ~WriteNC();
 
    //! Writes out a file
    ErrorCode write_file( const char* file_name,
                          const bool overwrite,
                          const FileOptions& opts,
                          const EntityHandle* output_list,
                          const int num_sets,
                          const std::vector< std::string >& qa_list,
                          const Tag* tag_list  = NULL,
                          int num_tags         = 0,
                          int export_dimension = 3 );
 
  private:
    //! ENTLOCNSEDGE for north/south edge
    //! ENTLOCWEEDGE for west/east edge
    enum EntityLocation
    {
        ENTLOCVERT = 0,
        ENTLOCNSEDGE,
        ENTLOCEWEDGE,
        ENTLOCFACE,
        ENTLOCSET,
        ENTLOCEDGE,
        ENTLOCREGION
    };
 
    class AttData
    {
      public:
        AttData() : attId( -1 ), attLen( 0 ), attVarId( -2 ), attDataType( NC_NAT ) {}
        int attId;
        NCDF_SIZE attLen;
        int attVarId;
        nc_type attDataType;
        std::string attValue;
    };
 
    class VarData
    {
      public:
        VarData() : varId( -1 ), numAtts( -1 ), entLoc( ENTLOCSET ), numLev( 0 ), sz( 0 ), has_tsteps( false ) {}
        int varId;
        int numAtts;
        nc_type varDataType;
        std::vector< int > varDims;  // The dimension indices making up this multi-dimensional variable
        std::map< std::string, AttData > varAtts;
        std::string varName;
        std::vector< Tag > varTags;            // Tags created for this variable, e.g. one tag per timestep
        std::vector< void* > memoryHogs;       // These will point to the real data; fill before writing the data
        std::vector< NCDF_SIZE > writeStarts;  // Starting index for writing data values along each dimension
        std::vector< NCDF_SIZE > writeCounts;  // Number of data values to be written along each dimension
        int entLoc;
        int numLev;
        int sz;
        bool has_tsteps;  // Indicate whether timestep numbers are appended to tag names
    };
 
    //! This info will be reconstructed from metadata stored on conventional fileSet tags
    //! Dimension names
    std::vector< std::string > dimNames;
 
    //! Dimension lengths
    std::vector< int > dimLens;
 
    //! Will collect used dimensions (coordinate variables)
    std::set< std::string > usedCoordinates;
 
    //! Dummy variables (for dimensions that have no corresponding coordinate variables)
    std::set< std::string > dummyVarNames;
 
    //! Global attribs
    std::map< std::string, AttData > globalAtts;
 
    //! Variable info
    std::map< std::string, VarData > varInfo;
 
    ErrorCode parse_options( const FileOptions& opts,
                             std::vector< std::string >& var_names,
                             std::vector< std::string >& desired_names,
                             std::vector< int >& tstep_nums,
                             std::vector< double >& tstep_vals );
    /*
     * Map out the header, from tags on file set; it is the inverse process from
     * ErrorCode NCHelper::create_conventional_tags
     */
    ErrorCode process_conventional_tags( EntityHandle fileSet );
 
    ErrorCode process_concatenated_attribute( const void* attPtr,
                                              int attSz,
                                              std::vector< int >& attLen,
                                              std::map< std::string, AttData >& attributes );
 
    //! Interface instance
    Interface* mbImpl;
    WriteUtilIface* mWriteIface;
 
    //! File var
    const char* fileName;
 
    //! File numbers assigned by (p)netcdf
    int fileId;
 
    //! Debug stuff
    DebugOutput dbgOut;
 
#ifdef MOAB_HAVE_MPI
    ParallelComm* myPcomm;
#endif
 
    //! Write options
    bool noMesh;
    bool noVars;
    bool append;
 
    //! Cached tags for writing. This will be important for ordering the data, in parallel
    Tag mGlobalIdTag;
 
    //! Are we writing in parallel? (probably in the future)
    bool isParallel;
 
    //! CAM Euler, etc,
    std::string grid_type;
 
    //! Helper class instance
    NCWriteHelper* myHelper;
};
 
}  // namespace moab
 
#endif